PFO_beta_C - PFAM28P - GREMLIN Contacts

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PFO_beta_C - Pyruvate ferredoxin oxidoreductase beta subunit C terminal

PFAM:	PF12367	Sequences: CVTFNKVNTYDWYKERVYKLEEDGHDPTDREAAMEKALEWGDKIPIGVFYREERPTYEERLPVLKE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	66 (64)
Sequences:	11917 (7519)
Seq/√Len:	939.9
META:	0.949

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_E	35_E	3.682	1.00
32_A	35_E	2.815	1.00
18_Y	43_K	2.658	1.00
18_Y	45_P	2.076	1.00
36_K	39_E	2.054	1.00
17_V	46_I	1.899	1.00
27_P	51_R	1.874	1.00
11_D	15_E	1.870	1.00
30_R	34_M	1.743	1.00
12_W	16_R	1.712	1.00
56_T	59_E	1.701	1.00
28_T	51_R	1.675	1.00
31_E	38_L	1.629	1.00
34_M	38_L	1.610	1.00
19_K	22_E	1.544	1.00
5_N	8_N	1.507	1.00
19_K	46_I	1.468	1.00
32_A	36_K	1.440	1.00
2_V	10_Y	1.405	1.00
29_D	32_A	1.311	1.00
39_E	43_K	1.258	1.00
10_Y	14_K	1.251	1.00
55_P	60_R	1.234	1.00
30_R	38_L	1.210	1.00
20_L	36_K	1.193	1.00
5_N	9_T	1.144	1.00
25_H	36_K	1.114	1.00
48_V	51_R	1.107	1.00
40_W	44_I	1.065	1.00
20_L	25_H	1.043	1.00
17_V	44_I	1.039	1.00
28_T	52_E	1.035	1.00
39_E	45_P	1.025	1.00
6_K	9_T	1.004	1.00
57_Y	61_L	0.956	1.00
33_A	50_Y	0.937	1.00
8_N	12_W	0.936	1.00
20_L	49_F	0.934	1.00
18_Y	39_E	0.927	1.00
5_N	13_Y	0.925	1.00
36_K	49_F	0.891	1.00
31_E	34_M	0.867	1.00
28_T	53_E	0.855	1.00
36_K	45_P	0.852	1.00
18_Y	23_D	0.842	1.00
58_E	63_V	0.818	1.00
54_R	60_R	0.813	1.00
39_E	42_D	0.803	1.00
25_H	33_A	0.799	1.00
35_E	39_E	0.784	1.00
25_H	29_D	0.779	1.00
26_D	32_A	0.771	1.00
16_R	42_D	0.767	1.00
56_T	60_R	0.752	1.00
21_E	24_G	0.747	1.00
13_Y	61_L	0.738	1.00
26_D	29_D	0.726	1.00
21_E	36_K	0.707	1.00
12_W	15_E	0.700	1.00
45_P	49_F	0.696	1.00
11_D	14_K	0.696	1.00
55_P	59_E	0.686	1.00
30_R	37_A	0.679	1.00
53_E	59_E	0.661	1.00
10_Y	17_V	0.654	1.00
35_E	38_L	0.645	1.00
60_R	63_V	0.636	1.00
16_R	44_I	0.631	1.00
23_D	43_K	0.628	1.00
2_V	9_T	0.623	1.00
16_R	43_K	0.620	1.00
37_A	49_F	0.619	1.00
41_G	44_I	0.615	1.00
8_N	13_Y	0.614	1.00
6_K	10_Y	0.612	1.00
17_V	45_P	0.611	1.00
9_T	13_Y	0.603	1.00
52_E	56_T	0.594	1.00
14_K	19_K	0.586	1.00
29_D	33_A	0.584	1.00
1_C	4_F	0.573	1.00
9_T	12_W	0.573	1.00
8_N	14_K	0.573	1.00
5_N	12_W	0.560	1.00
25_H	32_A	0.557	1.00
13_Y	44_I	0.554	1.00
8_N	57_Y	0.552	1.00
30_R	50_Y	0.545	1.00
18_Y	36_K	0.541	1.00
58_E	64_L	0.536	1.00
5_N	10_Y	0.536	1.00
52_E	55_P	0.535	1.00
37_A	40_W	0.530	1.00
44_I	49_F	0.521	1.00
23_D	36_K	0.503	1.00
45_P	48_V	0.500	1.00

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
3c2gA	1	0.6061	9.4	0.87	Contact Map
4pa0A	1	0.9242	8.1	0.874	Contact Map
4qbdA	1	0.9242	7.9	0.874	Contact Map
1kk8A	1	0.9242	7.6	0.875	Contact Map
2oo9A	2	0.697	7.4	0.876	Contact Map
2datA	1	0.3636	7.4	0.876	Contact Map
2v26A	1	0.9394	6.6	0.879	Contact Map
1h7nA	5	0.7879	6.5	0.879	Contact Map
1r8jA	2	0.8182	6.5	0.88	Contact Map
2ycuA	1	0.9545	6.2	0.88	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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